Contacts of the helix formed by residues 313 - 340 (chain A) in PDB entry 4KYI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 1.3 77.3 - - - +
314A GLY* 1.3 56.7 + - - +
315A THR* 4.4 7.0 - - + +
316A ALA* 3.7 17.1 - - + +
317A PHE* 2.7 32.1 + - - +
375A ASN* 4.3 0.2 - - - -
376A THR* 3.6 8.5 - - - -
380A THR* 6.1 4.0 - - + -
245C LYS* 6.5 0.9 - - + -
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA* 1.3 72.9 - - - +
315A THR* 1.3 61.6 + - - +
317A PHE* 3.4 1.6 + - - +
318A GLU* 3.2 33.6 + - - +
375A ASN* 3.4 21.6 + - - -
376A THR* 3.9 5.7 + - - -
377A GLY* 4.4 12.6 + - - +
380A THR* 5.7 2.4 - - - +
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA* 3.3 6.2 - - + +
314A GLY* 1.3 75.1 - - - +
316A ALA* 1.3 66.3 + - - +
318A GLU* 4.1 8.0 - - - +
319A ASP* 3.1 26.3 + - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 3.9 14.8 - - + +
313A ALA* 3.2 26.3 + - + +
315A THR* 1.3 83.3 + - - +
317A PHE* 1.3 62.6 + - - +
319A ASP* 4.0 5.5 - - - +
320A ARG* 3.5 18.9 + - - +
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Residues in contact with PHE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 3.8 11.9 + - + +
313A ALA 2.7 17.6 + - - +
314A GLY 3.6 4.7 - - - +
316A ALA* 1.3 76.7 - - - +
318A GLU* 1.3 70.8 + - + +
320A ARG* 3.2 21.3 + - - +
321A VAL* 3.1 38.3 + - + +
373A TYR* 3.7 31.4 - - + -
374A ILE 4.1 4.5 - - - -
375A ASN* 3.6 47.6 - - + -
397A ASN* 4.3 6.3 - - - -
401A GLN* 3.3 30.1 - - - -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLY 3.2 18.2 + - - +
315A THR* 4.3 7.6 - - - +
317A PHE* 1.3 89.1 - - + +
319A ASP* 1.3 57.9 - - - +
321A VAL* 3.8 4.7 - - - -
322A ASN* 2.8 47.0 + - - +
375A ASN* 4.9 7.0 + - - +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A THR 3.1 20.3 + - - +
316A ALA* 4.0 7.6 - - - +
318A GLU* 1.3 78.1 - - - +
320A ARG* 1.3 60.5 + - - +
322A ASN* 4.0 6.0 - - - +
323A LYS* 3.1 48.2 + - - +
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 2.5 37.5 + - - +
316A ALA 3.5 8.5 + - - +
317A PHE* 3.2 23.9 + - - +
319A ASP* 1.3 75.8 - - - +
321A VAL* 1.3 87.1 + - - +
323A LYS* 3.6 9.9 + - - +
324A ALA* 3.3 21.6 + - + +
373A TYR* 3.6 53.2 - - - +
401A GLN* 4.3 6.5 - - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 3.1 37.1 + - + +
318A GLU* 3.3 6.3 + - - +
320A ARG* 1.3 99.6 - - - +
322A ASN* 1.3 61.9 + - - +
324A ALA* 3.2 7.4 + - + +
325A LYS* 2.9 57.3 + - + +
401A GLN* 5.2 1.8 - - - +
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Residues in contact with ASN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 2.8 37.6 + - - +
319A ASP* 4.0 6.5 - - - +
321A VAL* 1.3 75.9 - - - +
323A LYS* 1.3 58.6 + - + +
324A ALA 3.0 4.7 - - - -
325A LYS* 3.3 19.3 + - - +
326A GLN* 2.9 33.0 + - - +
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Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ASP* 3.1 40.8 + - - +
320A ARG* 4.0 8.1 - - - +
321A VAL 3.4 0.4 - - - -
322A ASN* 1.3 75.3 - - + +
324A ALA* 1.3 57.6 + - - +
326A GLN* 4.0 18.8 - - - +
327A SER* 3.6 19.9 + - - -
361A ARG* 3.9 16.9 + - - +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ARG* 3.3 12.6 + - + +
321A VAL* 3.2 11.0 + - + +
322A ASN 3.0 0.4 - - - -
323A LYS* 1.3 78.3 - - - +
325A LYS* 1.3 64.8 + - + +
326A GLN 3.1 1.1 - - - -
327A SER 3.6 1.4 + - - +
328A ALA* 3.2 24.9 + - - +
361A ARG* 4.2 19.7 - - - +
557A LYS* 5.1 0.4 + - - -
604A GOL 4.2 6.5 + - - +
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A VAL* 2.9 42.8 + - + +
322A ASN* 3.8 18.0 + - - +
324A ALA* 1.3 76.9 - - + +
326A GLN* 1.3 59.8 + - - +
329A MET* 3.2 32.5 + - + +
557A LYS* 4.0 25.5 - - - +
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASN* 2.9 16.4 + - - +
323A LYS* 4.1 21.9 - - - +
325A LYS* 1.3 74.4 - - - +
327A SER* 1.3 56.7 + - - +
328A ALA 3.0 4.0 - - - -
329A MET* 3.0 34.0 + - + +
330A GLU* 3.0 35.1 + - + +
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS 3.6 14.9 + - - -
324A ALA 3.6 4.5 + - - -
326A GLN* 1.3 78.3 - - - +
328A ALA* 1.3 57.4 + - - +
330A GLU* 4.1 16.7 + - - +
331A ALA* 3.7 17.0 + - - +
360A ASN* 4.2 18.6 + - - +
361A ARG* 3.6 37.5 + - - +
604A GOL 4.3 8.6 + - - -
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA 3.2 17.0 + - - +
325A LYS 4.0 0.2 - - - +
326A GLN 3.0 0.8 - - - -
327A SER* 1.3 77.8 - - - +
329A MET* 1.3 64.1 + - - +
330A GLU 3.4 0.4 - - - -
331A ALA* 3.8 9.9 - - - +
332A ILE* 3.5 21.3 - - - +
543A GLU* 4.0 15.4 - - - +
557A LYS* 3.7 28.2 - - - +
604A GOL 3.8 19.3 - - - -
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Residues in contact with MET 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 3.2 23.0 + - + +
326A GLN* 3.0 21.2 + - + +
328A ALA* 1.3 78.5 - - - +
330A GLU* 1.3 60.6 + - + +
331A ALA 3.2 0.2 - - - -
332A ILE* 3.3 11.8 + - + +
333A SER* 3.0 26.0 + - - -
557A LYS* 4.3 14.8 - - + -
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLN* 3.0 36.4 + - + +
327A SER* 4.3 15.2 + - - +
328A ALA 3.4 0.2 - - - -
329A MET* 1.3 76.9 - - + +
331A ALA* 1.3 57.3 + - - +
333A SER* 3.8 9.2 - - - -
334A TRP* 2.7 59.0 + - + +
359A LEU* 6.1 1.2 - - - +
360A ASN* 5.4 6.4 - - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A SER 3.7 10.1 + - - +
328A ALA* 3.8 11.9 - - - +
330A GLU* 1.3 81.0 - - - +
332A ILE* 1.3 58.6 + - + +
334A TRP* 4.3 5.2 - - - +
335A PHE* 3.7 17.0 + - - +
359A LEU 5.7 4.0 - - - -
360A ASN 6.3 0.2 - - - +
539A TRP 4.5 2.3 - - - +
541A PRO* 4.1 22.1 - - + +
542A ILE* 5.5 0.9 - - + +
543A GLU* 5.9 2.2 - - + -
604A GOL 3.7 24.0 - - - +
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ALA 3.5 17.9 - - - +
329A MET* 3.3 10.1 + - + +
330A GLU 3.2 0.4 - - - -
331A ALA* 1.3 74.7 - - + +
333A SER* 1.3 65.6 + - - +
335A PHE* 3.3 10.3 + - + +
336A LYS* 3.1 31.5 + - - +
541A PRO* 4.7 18.8 - - + -
543A GLU* 5.0 4.9 - - + +
553A ALA 6.6 0.2 - - - -
554A GLN* 5.9 0.9 - - - -
555A ASP* 4.9 5.8 - - + +
556A PHE* 3.4 61.7 - - + +
557A LYS* 4.2 9.4 - - + -
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET 3.0 16.0 + - - -
330A GLU* 3.1 11.4 + - - -
332A ILE* 1.3 78.4 - - - +
334A TRP* 1.3 53.3 + - - +
336A LYS* 3.3 9.9 + - - +
337A ALA* 2.8 35.3 + - - +
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Residues in contact with TRP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLU* 2.7 51.0 + - + +
331A ALA* 4.3 4.9 - - - +
333A SER* 1.3 75.1 - - - +
335A PHE* 1.3 59.5 + - - +
337A ALA* 3.5 15.9 + - + +
338A ARG* 3.2 19.9 + - - +
355A THR* 4.1 35.4 - - + -
359A LEU* 3.7 45.5 - - + +
539A TRP* 3.9 40.6 - + + +
601A EDO 4.9 9.5 + - - -
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA 3.7 9.7 + - - +
332A ILE* 3.3 13.1 + - + +
333A SER 3.2 0.4 - - - -
334A TRP* 1.3 75.5 - - - +
336A LYS* 1.3 64.5 + - + +
337A ALA 3.1 1.3 - - - -
338A ARG* 2.9 20.0 + - - +
339A MET* 3.0 53.2 + - + +
536A ASN* 3.4 21.3 - - + -
539A TRP* 3.2 31.1 + - + +
540A ALA* 3.4 13.7 - - + -
541A PRO* 3.8 11.4 - - + -
553A ALA* 3.4 41.3 - - + -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.1 18.2 + - - +
333A SER* 3.7 10.6 - - - +
335A PHE* 1.3 85.2 - - + +
337A ALA* 1.3 57.1 + - - +
339A MET* 4.4 6.1 - - + +
340A ASP* 2.8 56.0 + - - +
556A PHE* 4.0 27.2 - - - -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER* 2.8 20.0 + - - +
334A TRP* 3.5 25.6 - - + +
335A PHE 3.1 0.2 - - - -
336A LYS* 1.3 78.7 - - - +
338A ARG* 1.3 55.7 + - - +
340A ASP* 4.1 4.3 - - - +
341A SER* 3.2 23.3 + - - -
601A EDO 3.7 8.0 + - - +
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Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TRP 3.2 11.3 + - - +
335A PHE 2.9 10.5 + - - +
337A ALA* 1.3 76.5 - - - +
339A MET* 1.3 62.5 + - - +
341A SER* 2.3 30.4 + - - +
342A LEU* 3.5 22.9 + - - +
519A GLU* 2.6 43.3 + - - -
532A THR 3.3 6.9 + - - -
535A LEU* 3.3 31.3 + - - +
536A ASN* 2.4 44.9 + - - +
539A TRP* 3.8 31.5 - - + +
601A EDO 3.7 24.7 + - - +
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Residues in contact with MET 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 3.0 53.1 + - + +
336A LYS* 3.4 6.5 + - + +
338A ARG* 1.3 79.0 - - - +
340A ASP* 1.3 63.4 + - - +
341A SER 3.2 0.2 - - - -
342A LEU* 3.3 29.6 - - + +
343A VAL* 4.8 3.3 - - - +
536A ASN* 3.3 40.2 - - + +
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Residues in contact with ASP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LYS* 2.8 43.5 + - - +
337A ALA* 4.1 5.2 - - - +
339A MET* 1.3 77.4 - - - +
341A SER* 1.3 61.5 + - - +
342A LEU 2.9 13.4 - - - +
343A VAL* 4.4 7.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il